[med-svn] r22712 - in trunk/packages/python-cogent/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Wed Aug 24 13:18:54 UTC 2016
Author: tille
Date: 2016-08-24 13:18:53 +0000 (Wed, 24 Aug 2016)
New Revision: 22712
Removed:
trunk/packages/python-cogent/trunk/debian/patches/cd-hit.patch
Modified:
trunk/packages/python-cogent/trunk/debian/changelog
trunk/packages/python-cogent/trunk/debian/control
trunk/packages/python-cogent/trunk/debian/patches/series
Log:
revert cd-hit name change in Debian
Modified: trunk/packages/python-cogent/trunk/debian/changelog
===================================================================
--- trunk/packages/python-cogent/trunk/debian/changelog 2016-08-24 11:46:48 UTC (rev 22711)
+++ trunk/packages/python-cogent/trunk/debian/changelog 2016-08-24 13:18:53 UTC (rev 22712)
@@ -4,6 +4,9 @@
* Fix watch file
* Fix homepage
* cme fix dpkg-control
+ * Build-Depends: python-setuptools
+ * revert cd-hit name change in Debian
+ Closes: #835213
-- Andreas Tille <tille at debian.org> Wed, 24 Aug 2016 13:42:46 +0200
Modified: trunk/packages/python-cogent/trunk/debian/control
===================================================================
--- trunk/packages/python-cogent/trunk/debian/control 2016-08-24 11:46:48 UTC (rev 22711)
+++ trunk/packages/python-cogent/trunk/debian/control 2016-08-24 13:18:53 UTC (rev 22712)
@@ -9,6 +9,7 @@
dh-python,
python-all-dev,
python-numpy,
+ python-setuptools,
python-sphinx,
cython,
blast2,
Deleted: trunk/packages/python-cogent/trunk/debian/patches/cd-hit.patch
===================================================================
--- trunk/packages/python-cogent/trunk/debian/patches/cd-hit.patch 2016-08-24 11:46:48 UTC (rev 22711)
+++ trunk/packages/python-cogent/trunk/debian/patches/cd-hit.patch 2016-08-24 13:18:53 UTC (rev 22712)
@@ -1,82 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Thu, 21 May 2015 08:47:01 +0200
-Bug-Debian: http://bugs.debian.org/730515
-Description: cd-hit-est is cdhit-est in Debian
- As the bug log shows cd-hit upstream was contacted about a consistent
- naming scheme. Since there was no answer I decided to keep the latest
- upstream naming scheme of cd-hit and adapt pyython-cogent (which is known
- to lag behind upstream changes (see raxml_unsupported_version.patch)
-
---- a/cogent/app/cd_hit.py
-+++ b/cogent/app/cd_hit.py
-@@ -201,7 +201,7 @@ class CD_HIT_EST(CD_HIT):
- Use this version of CD-HIT if your MolType is PROTEIN
- """
-
-- _command = 'cd-hit-est'
-+ _command = 'cdhit-est'
- _input_handler = '_input_as_multiline_string'
- _parameters = CD_HIT._parameters
- _parameters.update({\
---- a/tests/test_app/test_cd_hit.py
-+++ b/tests/test_app/test_cd_hit.py
-@@ -22,24 +22,24 @@ class CD_HIT_Tests(TestCase):
- """CD_HIT BaseCommand should return the correct BaseCommand"""
- c = CD_HIT()
- self.assertEqual(c.BaseCommand,\
-- ''.join(['cd "',getcwd(),'/"; ','cd-hit']))
-+ ''.join(['cd "',getcwd(),'/"; ','cdhit']))
- c.Parameters['-i'].on('seq.txt')
- self.assertEqual(c.BaseCommand,\
-- ''.join(['cd "',getcwd(),'/"; ','cd-hit -i "seq.txt"']))
-+ ''.join(['cd "',getcwd(),'/"; ','cdhit -i "seq.txt"']))
- c.Parameters['-c'].on(0.8)
- self.assertEqual(c.BaseCommand,\
-- ''.join(['cd "',getcwd(),'/"; ','cd-hit -c 0.8' +
-+ ''.join(['cd "',getcwd(),'/"; ','cdhit -c 0.8' +
- ' -i "seq.txt"']))
-
- def test_changing_working_dir(self):
- """CD_HIT BaseCommand should change according to WorkingDir"""
- c = CD_HIT(WorkingDir='/tmp/cdhit_test')
- self.assertEqual(c.BaseCommand,\
-- ''.join(['cd "','/tmp/cdhit_test','/"; ','cd-hit']))
-+ ''.join(['cd "','/tmp/cdhit_test','/"; ','cdhit']))
- c = CD_HIT()
- c.WorkingDir = '/tmp/cdhit_test2'
- self.assertEqual(c.BaseCommand,\
-- ''.join(['cd "','/tmp/cdhit_test2','/"; ','cd-hit']))
-+ ''.join(['cd "','/tmp/cdhit_test2','/"; ','cdhit']))
-
- #removing the dirs is proof that they were created at the same time
- #if the dirs are not there, an OSError will be raised
-@@ -58,24 +58,24 @@ class CD_HIT_EST_Tests(TestCase):
- """CD_HIT_EST BaseCommand should return the correct BaseCommand"""
- c = CD_HIT_EST()
- self.assertEqual(c.BaseCommand,\
-- ''.join(['cd "',getcwd(),'/"; ','cd-hit-est']))
-+ ''.join(['cd "',getcwd(),'/"; ','cdhit-est']))
- c.Parameters['-i'].on('seq.txt')
- self.assertEqual(c.BaseCommand,\
-- ''.join(['cd "',getcwd(),'/"; ','cd-hit-est -i "seq.txt"']))
-+ ''.join(['cd "',getcwd(),'/"; ','cdhit-est -i "seq.txt"']))
- c.Parameters['-c'].on(0.8)
- self.assertEqual(c.BaseCommand,\
-- ''.join(['cd "',getcwd(),'/"; ','cd-hit-est -c 0.8' +
-+ ''.join(['cd "',getcwd(),'/"; ','cdhit-est -c 0.8' +
- ' -i "seq.txt"']))
-
- def test_changing_working_dir(self):
- """CD_HIT_EST BaseCommand should change according to WorkingDir"""
- c = CD_HIT_EST(WorkingDir='/tmp/cdhitest_test')
- self.assertEqual(c.BaseCommand,\
-- ''.join(['cd "','/tmp/cdhitest_test','/"; ','cd-hit-est']))
-+ ''.join(['cd "','/tmp/cdhitest_test','/"; ','cdhit-est']))
- c = CD_HIT_EST()
- c.WorkingDir = '/tmp/cdhitest_test2'
- self.assertEqual(c.BaseCommand,\
-- ''.join(['cd "','/tmp/cdhitest_test2','/"; ','cd-hit-est']))
-+ ''.join(['cd "','/tmp/cdhitest_test2','/"; ','cdhit-est']))
-
- #removing the dirs is proof that they were created at the same time
- #if the dirs are not there, an OSError will be raised
Modified: trunk/packages/python-cogent/trunk/debian/patches/series
===================================================================
--- trunk/packages/python-cogent/trunk/debian/patches/series 2016-08-24 11:46:48 UTC (rev 22711)
+++ trunk/packages/python-cogent/trunk/debian/patches/series 2016-08-24 13:18:53 UTC (rev 22712)
@@ -6,4 +6,3 @@
fasttree_not_in_caps.patch
raxml_unsupported_version.patch
# debug_tests.patch
-cd-hit.patch
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